Protein-protein interactions are often mediated by weak and transient protein-peptide interactions. Determining the binding specificity of protein-peptide recognition poses a great challenge to computer modeling. A computational approach that combines energetic representation of the interaction interface and statistical selection of informative features characterizing the recognition mode will be presented for studying modular domain and peptide interactions. This approach connects all-atom structure modeling and free energy calculation to systems level understanding of biological regulations. We will present our recent attempt to improve the scoring function particularly the solvation energy in calculating the energetic terms of protein-peptide interactions. In addition, the application of this approach to multiple systems will be shown to illustrate its usefulness in facilitate decoding the binding specificity of protein recognition.

Determining the binding specificity of protein-peptide recognition

244th National Meeting (2012)

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